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This Week in Genome Biology: Dec 31, 2014

Through single molecule analyses on multiple sections each from more than a dozen glial tumors, a University of Washington-led team detected regional differences in mutational patterns within tumors. The researchers used a single molecule molecular inversion probe assay to assess cancer-related gene mutations and/or amplifications in three to five regions apiece from 10 grade IV glioma tumors, three grade III gliomas, and one grade II astrocytoma. The search revealed intra-tumor heterogeneity in three of the cases, the study's authors note, highlighting the "need to sample multiple regions in [glioblastoma] and other glial tumors when devising personalized treatments based on genomic information."

Researchers from China took an integrated look at genetic and epigenetic profiles in hepatocellular carcinoma (HCC) tumors and cell lines. Using a combination of liquid chromatography, tandem mass spectrometry, and multiple sequencing methods, the team profiled DNA mutations and copy number changes along with 5-methylcytosine and 5-hydroxymethylcytosine patterns in matched tumor and normal samples from 16 individuals with HCC and in two HCC-derived cell lines. In the process, investigators identified half a dozen genes with potential tumor suppressor roles as well as signaling pathways that appear prone to epigenetic glitches in HCC.

An international team used genome sequencing and resequencing to track genomic signatures associated with population declines and recovery in the once endangered crested ibis, a bird species native to Northeastern Asia that reached a low of two wild breeding pairs in the early 1990s. After producing reference genomes for the crested ibis and the little egret, a related species from the same region that's not endangered, the researchers resequenced six more crested ibis and six little egret representatives. By comparing the sequences to one another and to sequences from previously sequenced bird species, the group saw signs of lower-than-usual genetic diversity and higher-than-usual accumulation of deleterious mutations in the endangered crested ibis, ultimately tracking down a genetic signature that seems to be shared across endangered bird species.